Primary immunodeficiency or monogenic inflammatory bowel disease
Gene: LATComment on list classification: Changed rating of gene from Red to Green. This gene was rated as Green in v2.208 and incorrectly automatically demoted to Red in v2.209. This was due to a defect in the automatic PanelApp uploading tool when a set of publications was added to the panel with the source ‘Other’, and under certain conditions associated to previous sources listed, resulted in the rating of the gene being automatically changed when it should not have been.Created: 14 Oct 2020, 1:15 p.m. | Last Modified: 14 Oct 2020, 1:15 p.m.
Panel Version: 2.269
The following PubMed IDs were added to gene LAT (OMIM gene MIM#602354): 27522155. These publications have been associated with the gene by the immunodeficiencies subgroup of the Human Phenotype Ontology Immune Mediated Disorders Consortium (https://hpo-immune-mediated-disorders.groups.io/g/update) in August 2020.Created: 13 Oct 2020, 9:36 a.m. | Last Modified: 13 Oct 2020, 9:36 a.m.
Panel Version: 2.208
Publications
agree with green geneCreated: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
YES- this is covered on our targeted exomeCreated: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
Gene rating submitted by Kimberly Gilmour and Austen Worth on behalf of London North GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email 6th September the Specialist Test Group all agreed there is enough evidence to rate this gene Green.Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
Gene rating submitted by Tracy Briggs, David Gokhale and Abigal Rousseau on behalf of North West GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email on 20th June the Specialist Test Group all agreed there is enough evidence to rate this gene Green.Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
Comment on list classification: Changed Amber to Green. After internal clinical review it was agreed that as there are two unrelated cases, two variants (frameshifting) and a supportive mouse model for T cell deficits plus a Green rating from external expert review this gene could be promoted to GreenCreated: 11 Jul 2018, 4:09 p.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): LAT .PanelApp HGNC gene symbol check: LAT . IUIS Disease: LAT deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: Nl to low, .IUIS Other affected cells: N/A. IUIS Associated features: Adenopathy, splenomegaly, recurrent infections, autoimmunity. IUIS Major category: Immunodeficiencies affecting cellular and humoral immunity. IUIS Subcategory: T-B+ Severe Combined Immune Deficiency (SCID)Created: 2 Jul 2018, 10:35 a.m.
This gene was present in the original PanelApp PID panel dataset (review in April 2018) rated as Amber. The gene is absent from external expert immunodeficiency diagnostic gene list(s) GOSH or GRID. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1.Created: 20 Apr 2018, 10:30 a.m.
Comment on list classification: 2 independent cases and 2 variants (a 2 bp deletion and a 1 bp insertion) reported in OMIM: 1 Arab family in Keller et al 2016/PMID:27242165, and 1 Pakistani family in Bacchelli et al 2017/PMID:27522155). No more current publications and not yet associated with a disease in DD-G2P. Therefore currently insufficient cases to rate green so rated as Amber and added 'watchlist' tag in anticipation of further publications.Created: 29 Aug 2017, 9:31 a.m.
Added to this panel as advised by Helen Brittain after a new gene-disorder association was reported in OMIM in June 2017 (Immunodeficiency 52, MIM:617514).Created: 29 Aug 2017, 9:26 a.m.
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
Immunodeficiency 52, 617514
Publications
Gene: lat has been classified as Green List (High Evidence).
Source Other was added to LAT. Publications for gene LAT were updated from 27522155; 27242165 to 27522155; 27242165 Rating Changed from Green List (high evidence) to Red List (low evidence)
Source NHS GMS was added to LAT.
Source North West GLH was added to LAT.
Source London North GLH was added to LAT.
2018-07-12 Louise Daugherty (Genomics England Curator) promoted panel to v1.0. Reviews were assessed, and panel was revised according to expert reviews and further in-house curation based on PanelApp guidelines. Previous panels (A- or hypo-gammaglobulinaemia, Congenital neutropaenia, Agranulocytosis, Combined B and T cell defect, Inherited complement deficiency and SCID panels) that were merged with this panel, were checked again for any changes/new reviews prior to versioning of this panel, these merged panels are now retired/made internal.
Gene: lat has been classified as Green List (High Evidence).
Phenotypes for gene LAT were set to Immunodeficiency 52, 617514, Adenopathy, splenomegaly, recurrent infections, autoimmunity, Immunodeficiencies affecting cellular and humoral immunity
IUIS Classification February 2018 was added to LAT. Panel: Primary immunodeficiency disorders
SCID v1.6 was added to LAT. Panel: Primary immunodeficiency disorders
Combined B and T cell defect v1.12 was added to LAT. Panel: Primary immunodeficiency disorders
LAT was added to Primary immunodeficiency disorders panel. Sources: Expert Review Amber, A- or hypo-gammaglobulinaemia v1.25
LAT was created by Louise Daugherty